Many differences:
1. Religious: The Pilgrims who settled at Plymouth were "Puritans" vs. Anglicans at Jamestown. Plus, Plymouth was founded for religious reasons while Jamestown was founded for economic reasons. Don't get me wrong--religion was critical for both groups but the Puritans left England because they were religious outcasts while the settlers at Jamestown were there for economic benefit and had investors.
2. Economic/Agricultural: The Plymouth settlement was mostly self-sufficient while Jamestown depended on England for supplies of key items. The longer growing season at Jamestown led to the development of extensive plantations in Virginia. While initially both colonies began by focusing on fishing, the NE settlers moved into lumber or other businesses (mills for instance that were water-powered)
3. Role of the military: Jamestown was initially settled under martial law and the military played a significant role (especially in terms of governance) within the colony while the military presence for Plymouth was more of militia and didn't grow until the colony spread beyond Plymouth.
4. Demographics. Virginia was almost entirely English. New England saw Dutch settlers (in fact the Plymouth descendents began to worry that their children were being corrupted by the "lax" Dutch lifestyle).
5. Disease. More swamps, longer warm-weather seasons meant more mosquitoes in Virginia. The English settlers there came primarily from swampy areas of the UK and had been exposed to malaria previously. New research on the settlement suggests that one reason the settlers weren't attacked and anhiliated by Indians (and why their numbers retreated back into the forests) was the sudden onset of malaria (a disease that did not exist in this part of the New World prior to the appearance of the English). But the settlers in Plymouth came to an area that had been devastated by disease earlier (thus wiping out most of the indigenous peoples).
6. Culturally. Life was hard for both colonies. But the puritans in Plymouth were more of a culture of cooperation and sharing which helped ease relations with the Indians and allowed them to weather the longer winters in NE better than the more mercenary nature of the Jamestown settlers.
